seq region synonym code

modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm

+=head1 LICENSE
+
+  Copyright (c) 1999-2010 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <dev@ensembl.org>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+INTO 
+=cut
+
+package Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor;
+use vars qw(@ISA);
+use strict;
+
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::SeqRegionSynonym;
+
+@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
+
+
+sub get_synonyms{
+  my $self = shift;
+  my $seq_id = shift;
+  
+  my @results;
+
+  my $sth = $self->prepare("select seq_region_synonym_id, synonym, external_db_id from seq_region_synonym where seq_region_id = ?");
+  $sth->bind_param(1, $seq_id, SQL_INTEGER);
+  $sth->execute();
+  my $dbid;
+  my $alt_name;
+  my $ex_db;
+  $sth->bind_columns(\$dbid, \$alt_name, \$ex_db);
+  while($sth->fetch()){
+    push @results, Bio::EnsEMBL::SeqRegionSynonym->new(-adaptor => $self,
+                                                       -synonym => $alt_name,
+						       -dbID => $dbid,
+                                                       -external_db_id => $ex_db,
+                                                       -seq_region_id => $seq_id);
+  }
+  $sth->finish;
+
+  return \@results;
+}
+
+sub store {
+  my $self = shift;
+  my $syn = shift;
+
+  return if($syn->is_stored($self->db));
+
+  if(!defined($syn->seq_region_id)){
+    throw("seq_region_id is needed to store a seq_region_synoym");
+  }
+
+  my $sth = $self->prepare("INSERT IGNORE INTO seq_region_synonym (seq_region_id, synonym, external_db_id) VALUES (?, ?, ?)");
+  $sth->bind_param(1, $syn->seq_region_id,  SQL_INTEGER);
+  $sth->bind_param(2, $syn->name         ,  SQL_VARCHAR);
+  $sth->bind_param(3, $syn->external_db_id, SQL_INTEGER);
+  $sth->execute;
+  $syn->{'dbID'} = $sth->{'mysql_insertid'};
+  $sth->finish;
+}
+
+
+
+1;

modules/Bio/EnsEMBL/SeqRegionSynonym.pm

+=head1 LICENSE
+
+  Copyright (c) 1999-2010 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <dev@ensembl.org>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::SeqRegionSynonym -
+Object representing an alternatice name.
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+This object holds information about alternative name to
+Ensembl seq regions.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SeqRegionSynonym;
+
+use strict;
+use warnings;
+no warnings qw(uninitialized);
+
+use Bio::EnsEMBL::Storable;
+use Bio::Annotation::DBLink;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(deprecate);
+
+our @ISA = qw(Bio::EnsEMBL::Storable);
+
+=head2 new
+
+  Args [...] : list of named parameters 
+  Example    : my $srs = new Bio::EnsEMBL::SeqRegionSynonym(
+                    -adaptor => $adaptor,
+                    -synonym => $alt_name,
+                    -external_db_id => 1234
+                    -seq_region_id  => 12);
+  Description: Creates a new SeqRegionSynonym object
+  Returntype : Bio::EnsEMBL::SeqRegionSynonym
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::SeqRegionSynonymAdaptor
+  Status     : At Risk
+=cut
+
+sub new {
+  my ($class, @args) = @_;
+  
+  my $self = bless {},$class;
+
+  my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid) =
+    rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID'], @args );
+
+  $self->{'adaptor'} = $adaptor;
+
+  if( defined $ex_db ) { $self->external_db_id( $ex_db ) }
+  if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) }
+  if (defined $dbid) { $self->{'dbID'} = $dbid}
+
+  if( defined $synonym ) { 
+    $self->name( $synonym ) ;
+  } else {
+    warn "No alternative name given\n";
+    return undef;
+  }
+
+  return $self;
+}
+
+sub name{
+ my $self = shift;
+  $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+sub external_db_id{
+ my $self = shift;
+  $self->{'ex_db'} = shift if(@_);
+  return $self->{'ex_db'};
+}
+
+sub seq_region_id{
+  my $self = shift;
+  $self->{'seq_region_id'} = shift if(@_);
+  return $self->{'seq_region_id'};
+}
+
+1;